Being that you use mods, I'm wondering if maybe it's a problem that learned engrams have overextended what points you would have at your level?
This isn't the behavior I normally see with that though. To verify if its a mod causing it I would do the following.
1) Write down all of the mods.
2) Backup your level and character saves somewhere safe (You can put the backups back in later)
3) First remove all mods, if your engram points go back to normal it's definitely a mod causing it
4) To find out which one, put them all back on and start removing them and testing one by one.